Education Minister Jeff Johnson says the money will be made available if a school can show it needs flood mitigation not covered by insurance.
Such measures may include landscaping or site remediation, relocation of electrical equipment or flood-proof doors and windows.
The flood-damaged schools eligible for the cash include Elbow Park, Rideau Park and St. Mary's in Calgary.
The High River schools that could benefit are Holy Spirit Academy, Notre Dame Collegiate, Right Honourable Joe Clark School, Senator Riley School and Spitzee Elementary School.
All but three of the schools damaged in last June's floods have been repaired and are open to students.